https://github.com/fperraudeau/gphmm

Generalized Pair Hidden Markov Chain Model (GPHMM)
https://github.com/fperraudeau/gphmm

hmm hmm-model hmm-viterbi-algorithm sequence-alignment sequence-to-sequence

Last synced: 25 days ago
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Generalized Pair Hidden Markov Chain Model (GPHMM)

• Host: GitHub
• URL: https://github.com/fperraudeau/gphmm
• Owner: fperraudeau
• Created: 2017-04-27T18:48:06.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2017-12-05T03:37:26.000Z (almost 8 years ago)
• Last Synced: 2025-01-06T16:54:19.652Z (9 months ago)
• Topics: hmm, hmm-model, hmm-viterbi-algorithm, sequence-alignment, sequence-to-sequence
• Language: R
• Homepage:
• Size: 52.7 KB
• Stars: 1
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md

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README

          
# gphmm

Generalized Pair Hidden Markov Model (GPHMM)

[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)

[![Travis-CI Build Status](https://travis-ci.org/fperraudeau/gphmm.svg?branch=master)](https://travis-ci.org/fperraudeau/gphmm)

This package trains a GPHMM and computes GPHMM probabilities.

The model will is described in details in https://www.biorxiv.org/content/early/2017/12/04/228619.

## Installation

```{r}

install.packages('gphmm')

```

Note that `gphmm` package need compilation of C++ code.

Installing from CRAN is recommended. However, if you want to install the version from GitHub, you can do so with the following lines of code

```{r}

library(devtools)

install_github("fperraudeau/gphmm")

```